Returns a data frame with clinical codes that match the supplied regular expression. Ignores case by default.
code_descriptions_like(
reg_expr,
code_type,
all_lkps_maps = NULL,
ignore_case = TRUE,
codes_only = FALSE,
preferred_description_only = TRUE,
standardise_output = TRUE,
col_filters = default_col_filters()
)a regular expression to search for
character. The type of clinical code system to be searched. Must be one obnf, dmd, icd9, icd10, read2, read2_drugs, read3, opcs4, data_coding_3, data_coding_4, data_coding_5, data_coding_6, sct, or phecode)`.
Either a named list of lookup and mapping tables (either
data frames or tbl_dbi objects), or the path to a SQLite database
containing these tables (see also build_all_lkps_maps() and
all_lkps_maps_to_db()). If NULL, will attempt to connect to an SQLite
database named 'all_lkps_maps.db' in the current working directory, or to a
a SQLite database specified by an environmental variable named
'ALL_LKPS_MAPS_DB' (see
here
for how to set environment variables using a .Renviron file). The latter
method will be used in preference.
Should case differences be ignored in the match?
bool. If TRUE, return a character vector of
unique codes. If FALSE (default), return a data frame of all
results including code descriptions (useful for manual validation).
bool. Return only preferred descriptions
for clinical codes with synonyms. Default value is TRUE.
bool. If TRUE (default), outputs a data
frame with columns named 'code', 'description' and 'code_type'. Otherwise
returns a data frame with all columns for the relevant lookup sheet from
(UK Biobank
resource 592).
A named list where each name in the list refers to the
name of a lookup or mapping table. Each item is also a named list, where
the names refer to column names in the corresponding table, and the items
are vectors of values to filter for. For example, list(my_lookup_table = list(colA = c("A", "B")) will result in my_lookup_table being filtered
for rows where colA is either 'A' or 'B'. Uses default_col_filters() by
default. Set to NULL to remove all filters.
data frame by default, or a character vector of codes if
codes_only is TRUE.
# build dummy all_lkps_maps
all_lkps_maps_dummy <- build_all_lkps_maps_dummy()
# lookup ICD10 code descriptions matching 'cyst'
code_descriptions_like(
reg_expr = "cyst",
code_type = "icd10",
all_lkps_maps = all_lkps_maps_dummy
)
#> # A tibble: 2 × 3
#> code description code_type
#> <chr> <chr> <chr>
#> 1 L721 Trichilemmal cyst icd10
#> 2 N330 Tuberculous cystitis icd10